SubtiWiki - User contributions [en]

Akos T Kovacs

2024-01-26T07:23:00Z

Atkovacs: /* Publications in the last 10 years */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl] from 2012.

==Akos T Kovacs==
*Current position: Professor of Microbiome Ecology at Leiden University, the Netherlands (2023-)
*Previous positions:
*Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-2025, part time from 2023)
*Group leader at Friedrich Schiller University Jena, Germany (2012-2017)
*Habilitation (2016), PhD (2003)
*Contact: a.t.kovacs (AT) biology.leidenuniv.nl [mailto:a.t.kovacs@biology.leidenuniv.nl send mail]

==Research Interests==
*bacterial biofilm development
*plant microbiome
*chemical ecology, secondary metabolites, lipoeptides
*''B. subtilis'', ''B. cereus'', ''B. thuringiensis''
*interaction of ''Bacilli'' and fungi
*evolution in biofilms
*microbial cooperation and competition
*phenotypic heterogeneity

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Publications in the last 10 years==
<pubmed>38042415,38012258,37971263,37901115,37838789,37838589,37768063,37676037,37552953,37540742,37524911,37466402,37042030,36878770,35938723,35882195,35790818,35671583,35663012,35418164,35254137,35243332,34792377,34636664,34593997,34296794,34186025,34180604,33927051,33850233,33824496,33688015,33622852,33335606,33523996,33447807,33398098,33343000,33142084,33000496,32986513,32753507,32483306,32257302,31908831,33447794,31508511,33447790,31253991,31121908,31000489,30842767,30769118,30326845,30297741,29887307,29208748,29205129,29126191,29346268,29124898,29073022,28783117,28583948,28462927,28370801,28212310,28089324,27842347,27834716,27770951,27714933,27664741,27655338,27422364,27267987,27190142,27044625,26458398,26152584,26122431,25909364,25886351,25505463,25041820,24033913,25040940,24771632,24694715,24196425,24163345,23924781</pubmed>

==Homepages==
[https://www.universiteitleiden.nl/en/staffmembers/akos-kovacs#tab-1 UniversityPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2024-01-26T07:19:10Z

Atkovacs: /* Publications in the last 10 years */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl] from 2012.

==Akos T Kovacs==
*Current position: Professor of Microbiome Ecology at Leiden University, the Netherlands (2023-)
*Previous positions:
*Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-2025, part time from 2023)
*Group leader at Friedrich Schiller University Jena, Germany (2012-2017)
*Habilitation (2016), PhD (2003)
*Contact: a.t.kovacs (AT) biology.leidenuniv.nl [mailto:a.t.kovacs@biology.leidenuniv.nl send mail]

==Research Interests==
*bacterial biofilm development
*plant microbiome
*chemical ecology, secondary metabolites, lipoeptides
*''B. subtilis'', ''B. cereus'', ''B. thuringiensis''
*interaction of ''Bacilli'' and fungi
*evolution in biofilms
*microbial cooperation and competition
*phenotypic heterogeneity

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Publications in the last 10 years==
<pubmed> 38042415, 38012258, 37971263, 37901115, 37838789, 37838589, 37768063, 37676037, 37552953, 37540742, 37524911, 37466402, 37042030, 36878770, 35938723, 35882195, 35790818, 35671583, 35663012, 35418164, 35254137, 35243332, 34792377, 34636664, 34593997, 34296794, 34186025, 34180604, 33927051, 33850233, 33824496, 33688015, 33622852, 33335606, 33523996, 33447807, 33398098, 33343000, 33142084, 33000496, 32986513, 32753507, 32483306, 32257302, 31908831, 33447794, 31508511, 33447790, 31253991, 31121908, 31000489, 30842767, 30769118, 30326845, 30297741, 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==
[https://www.universiteitleiden.nl/en/staffmembers/akos-kovacs#tab-1 UniversityPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2024-01-26T07:18:54Z

Atkovacs: /* Publications in the last 10 years */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl] from 2012.

==Akos T Kovacs==
*Current position: Professor of Microbiome Ecology at Leiden University, the Netherlands (2023-)
*Previous positions:
*Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-2025, part time from 2023)
*Group leader at Friedrich Schiller University Jena, Germany (2012-2017)
*Habilitation (2016), PhD (2003)
*Contact: a.t.kovacs (AT) biology.leidenuniv.nl [mailto:a.t.kovacs@biology.leidenuniv.nl send mail]

==Research Interests==
*bacterial biofilm development
*plant microbiome
*chemical ecology, secondary metabolites, lipoeptides
*''B. subtilis'', ''B. cereus'', ''B. thuringiensis''
*interaction of ''Bacilli'' and fungi
*evolution in biofilms
*microbial cooperation and competition
*phenotypic heterogeneity

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Publications in the last 10 years==
<pubmed>38042415, 38012258, 37971263, 37901115, 37838789, 37838589, 37768063, 37676037, 37552953, 37540742, 37524911, 37466402, 37042030, 36878770, 35938723, 35882195, 35790818, 35671583, 35663012, 35418164, 35254137, 35243332, 34792377, 34636664, 34593997, 34296794, 34186025, 34180604, 33927051, 33850233, 33824496, 33688015, 33622852, 33335606, 33523996, 33447807, 33398098, 33343000, 33142084, 33000496, 32986513, 32753507, 32483306, 32257302, 31908831, 33447794, 31508511, 33447790, 31253991, 31121908, 31000489, 30842767, 30769118, 30326845, 30297741, 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==
[https://www.universiteitleiden.nl/en/staffmembers/akos-kovacs#tab-1 UniversityPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2024-01-26T07:18:26Z

Atkovacs:

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl] from 2012.

==Akos T Kovacs==
*Current position: Professor of Microbiome Ecology at Leiden University, the Netherlands (2023-)
*Previous positions:
*Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-2025, part time from 2023)
*Group leader at Friedrich Schiller University Jena, Germany (2012-2017)
*Habilitation (2016), PhD (2003)
*Contact: a.t.kovacs (AT) biology.leidenuniv.nl [mailto:a.t.kovacs@biology.leidenuniv.nl send mail]

==Research Interests==
*bacterial biofilm development
*plant microbiome
*chemical ecology, secondary metabolites, lipoeptides
*''B. subtilis'', ''B. cereus'', ''B. thuringiensis''
*interaction of ''Bacilli'' and fungi
*evolution in biofilms
*microbial cooperation and competition
*phenotypic heterogeneity

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Publications in the last 10 years==
<pubmed> 38042415, 38012258, 37971263, 37901115, 37838789, 37838589, 37768063, 37676037, 37552953, 37540742, 37524911, 37466402, 37042030, 36878770, 35938723, 35882195, 35790818, 35671583, 35663012, 35418164, 35254137, 35243332, 34792377, 34636664, 34593997, 34296794, 34186025, 34180604, 33927051, 33850233, 33824496, 33688015, 33622852, 33335606, 33523996, 33447807, 33398098, 33343000, 33142084, 33000496, 32986513, 32753507, 32483306, 32257302, 31908831, 33447794, 31508511, 33447790, 31253991, 31121908, 31000489, 30842767, 30769118, 30326845, 30297741, 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==
[https://www.universiteitleiden.nl/en/staffmembers/akos-kovacs#tab-1 UniversityPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2021-04-08T15:34:16Z

Atkovacs: Undo revision 210975 by Atkovacs (talk)

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current position: Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-)
*Habilitation (2016), PhD (2003)
*Contact: atkovacs@dtu.dk [mailto:atkovacs@dtu.dk send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2021)==
<pubmed> 33688015, 33824496, 33622852, 33335606, 33523996, 33447807, 33398098, 33343000, 33142084, 33000496, 32986513, 32753507, 32483306, 32257302, 31908831, 33447794, 31508511, 33447790, 31253991, 31121908, 31000489, 30842767, 30769118, 30326845, 30297741, 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==
[http://www.bioengineering.dtu.dk/english/researchny/research-sections/section-for-microbial-and-chemical-ecology/bacterial-interactions-and-evolution GroupPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2021-04-08T15:33:57Z

Atkovacs: Undo revision 210975 by Atkovacs (talk)

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current position: Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-)
*Habilitation (2016), PhD (2003)
*Contact: atkovacs@dtu.dk [mailto:atkovacs@dtu.dk send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2021)==
<pubmed> 33824496, 33688015, 33622852, 33335606, 33523996, 33447807, 33398098, 33343000, 33142084, 33000496, 32986513, 32753507, 32483306, 32257302, 31908831, 33447794, 31508511, 33447790, 31253991, 31121908, 31000489, 30842767, 30769118, 30326845, 30297741, 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==
[http://www.bioengineering.dtu.dk/english/researchny/research-sections/section-for-microbial-and-chemical-ecology/bacterial-interactions-and-evolution GroupPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2021-04-08T15:31:01Z

Atkovacs:

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current position: Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-)
*Habilitation (2016), PhD (2003)
*Contact: atkovacs@dtu.dk [mailto:atkovacs@dtu.dk send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus/thuringiensis''
*plant-microbe interaction
*interaction of Bacilli and fungi
*evolution in biofilms
*chemical ecology of Bacilli, secondary metabolites

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications from last 5 years (2015-2021)==
<pubmed> 33824496, 33688015, 33622852, 33335606, 33523996, 33447807, 33398098, 33343000, 33142084, 33000496, 32986513, 32753507, 32483306, 32257302, 31908831, 33447794, 31508511, 33447790, 31253991, 31121908, 31000489, 30842767, 30769118, 30326845, 30297741, 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25040940, 23924781 </pubmed>

==Homepages==
[http://www.bioengineering.dtu.dk/english/researchny/research-sections/section-for-microbial-and-chemical-ecology/bacterial-interactions-and-evolution GroupPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2018-07-30T11:47:24Z

Atkovacs: /* Homepages */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current position: Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-)
*Habilitation (2016), PhD (2003)
*Contact: atkovacs@dtu.dk [mailto:atkovacs@dtu.dk send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2018)==
<pubmed> 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==
[http://www.bioengineering.dtu.dk/english/researchny/research-sections/section-for-microbial-and-chemical-ecology/bacterial-interactions-and-evolution GroupPage]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2018-07-30T11:45:35Z

Atkovacs: /* Homepages */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current position: Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-)
*Habilitation (2016), PhD (2003)
*Contact: atkovacs@dtu.dk [mailto:atkovacs@dtu.dk send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2018)==
<pubmed> 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==
http://www.bioengineering.dtu.dk/english/researchny/research-sections/section-for-microbial-and-chemical-ecology/bacterial-interactions-and-evolution

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2018-07-30T11:43:35Z

Atkovacs: /* Recent publications (2014-2018) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current position: Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-)
*Habilitation (2016), PhD (2003)
*Contact: atkovacs@dtu.dk [mailto:atkovacs@dtu.dk send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2018)==
<pubmed> 29887307, 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2018-06-10T07:02:50Z

Atkovacs: /* Recent publications (2014-2017) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current position: Professor of Bacterial Physiology and Genetics at the Technical University of Denmark (2017-)
*Habilitation (2016), PhD (2003)
*Contact: atkovacs@dtu.dk [mailto:atkovacs@dtu.dk send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2018)==
<pubmed> 29208748, 29205129, 29126191, 29346268, 29124898, 29073022, 28783117, 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Roberto Grau

2017-10-31T08:28:35Z

Atkovacs: /* Publications */

==Roberto Grau==
*Current institution: Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas (FCByF), Universidad Nacional de Rosario (UNR), Argentina

==Research Interests==
* ''Bacillus subtilis''
* [[biofilm formation]]
* sporulation
* [[sliding]]
* bioremediation
* antimicrobial compounds

==Publications==
<pubmed>29073022,28435840,28294433,28134244, 26396299,26152584, 23170957,16740951,15805512,14761993,12603732,10629174,9334321,8022269,8326865</pubmed>

==Homepages==

The Grau Lab [http://www.microbiologyrosario.org/]

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2017-10-31T08:23:31Z

Atkovacs: /* Recent publications (2014-2017) */

Akos T Kovacs

2017-07-13T08:19:26Z

Atkovacs:

Akos T Kovacs

2017-06-07T14:56:45Z

Atkovacs: /* Recent publications (2014-2017) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena (2012-)
*Habilitation (2016), PhD (2003)
*Faculty member of International Max Planck Research School, '''IMPRS'''[http://imprs.ice.mpg.de/ext/index.php?id=home]
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2017)==
<pubmed> 28583948, 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Sliding

2017-05-08T06:50:13Z

Atkovacs: /* Key reviews */

Sliding motility is a passive form of surface spreading that does not require an active motor but instead relies on surfactants to reduce surface tension, enabling the colony to spread away from the origin, driven by the outward pressure of cell growth. {{PubMed|20694026}}. Sliding can be observed in wild isolates of ''Bacillus subtilis'' not expressing or deleted for [[hag]] gene {{PubMed|16545127}}. Sliding requires surfactin production and the presence of potassium in the medium {{PubMed|12949115}}. Further, sliding requires various components that are related to biofilm formation {{PubMed|26152584}}.

{{CategoryTree
|Parents=
* 4. [[Lifestyles]]
** 4.1. [[Exponential and early post-exponential lifestyles]]
|Neighbours=
* 4.1.1. [[Motility and chemotaxis]]
* 4.1.2. [[Swarming]]
* 4.1.3. [[Sliding]]
* 4.1.4. [[Biofilm formation]]
* 4.1.5. [[Genetic competence]]
|Related=

|}}

__TOC__
 

==Labs working on sliding==
* [[Daniel Kearns]]
* [[Roberto Kolter]]
* Ray Fall
* [[Akos T Kovacs]]
* [[Roberto Grau]]

==Key genes and operons involved in sliding==
* required for sliding in ''B. subtilis'' NCIB 3610 on MSggN medium
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
** ''[[tasA]]''
** ''[[srfAA]]''
** ''[[srfAB]]''
** ''[[ktrA]]''
** ''[[ktrB]]''
** ''[[ktrC]]''
** ''[[ktrD]]''

* required for sliding in ''B. subtilis'' natto wild type and ''B. subtilis'' NCIB 3610 ''hag'' derivative on LB medium
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
** ''[[bslA]]''
** ''[[srfAA]]''
** ''[[srfAC]]''

* regulation
** [[KinB]]
** [[KinC]]
** [[Spo0A]]

==Important original publications==
<pubmed> 26152584, 25894589, 21784632,19659723,16545127,16321950,12949115</pubmed>

==Key reviews==
<pubmed>28370801, 20694026, 22092493</pubmed>

=Back to [[categories]]=

Akos T Kovacs

2017-05-08T06:49:11Z

Atkovacs: /* Recent publications (2014-2017) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena (2012-)
*Habilitation (2016), PhD (2003)
*Faculty member of International Max Planck Research School, '''IMPRS'''[http://imprs.ice.mpg.de/ext/index.php?id=home]
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2017)==
<pubmed> 28462927, 28370801, 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2017-02-18T11:31:30Z

Atkovacs: /* Recent publications (2014-2017) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena (2012-)
*Habilitation (2016), PhD (2003)
*Faculty member of International Max Planck Research School, '''IMPRS'''[http://imprs.ice.mpg.de/ext/index.php?id=home]
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2017)==
<pubmed> 28212310, 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2017-01-17T13:03:41Z

Atkovacs: /* Recent publications (2014-2016) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena (2012-)
*Habilitation (2016), PhD (2003)
*Faculty member of International Max Planck Research School, '''IMPRS'''[http://imprs.ice.mpg.de/ext/index.php?id=home]
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2017)==
<pubmed> 28089324, 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2016-11-24T16:01:40Z

Atkovacs: /* Recent publications (2014-2016) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena (2012-)
*Habilitation (2016), PhD (2003)
*Faculty member of International Max Planck Research School, '''IMPRS'''[http://imprs.ice.mpg.de/ext/index.php?id=home]
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2016)==
<pubmed> 27842347, 27834716, 27770951, 27714933, 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2016-09-26T07:30:27Z

Atkovacs: /* Recent publications (2014-2016) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena (2012-)
*Habilitation (2016), PhD (2003)
*Faculty member of International Max Planck Research School, '''IMPRS'''[http://imprs.ice.mpg.de/ext/index.php?id=home]
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2016)==
<pubmed> 27664741, 27655338, 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2016-08-11T06:56:36Z

Atkovacs:

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl].

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena (2012-)
*Habilitation (2016), PhD (2003)
*Faculty member of International Max Planck Research School, '''IMPRS'''[http://imprs.ice.mpg.de/ext/index.php?id=home]
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*''Bacillus subtilis''
*''Bacillus cereus''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2016)==
<pubmed> 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
Email me for possibilities.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2016-08-11T06:52:20Z

Atkovacs: /* Recent publications (2014-2016) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl]; permission required for use.

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*transcription profiling of Bacilli
*''Bacillus subtilis''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2016)==
<pubmed> 27422364, 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
A three-year PhD position in Microbiology: "Phenotypic heterogeneity and population dynamics in biofilms" within the framework of the Priority Programme SPP 1617 - Phenotypic heterogeneity and sociomicrobiology of bacterial populations is available at the Institute of Microbiology, Friedrich Schiller University (FSU) Jena, starting in September 2015. More information at [https://sites.google.com/site/terrestrialbiofilms/home/open-positions].
Contact [mailto:akos-tibor.kovacs@uni-jena.de me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2016-06-10T07:09:01Z

Atkovacs: /* Recent publications (2014-2016) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl]; permission required for use.

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*transcription profiling of Bacilli
*''Bacillus subtilis''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2016)==
<pubmed> 27267987, 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
A three-year PhD position in Microbiology: "Phenotypic heterogeneity and population dynamics in biofilms" within the framework of the Priority Programme SPP 1617 - Phenotypic heterogeneity and sociomicrobiology of bacterial populations is available at the Institute of Microbiology, Friedrich Schiller University (FSU) Jena, starting in September 2015. More information at [https://sites.google.com/site/terrestrialbiofilms/home/open-positions].
Contact [mailto:akos-tibor.kovacs@uni-jena.de me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2016-05-31T11:38:00Z

Atkovacs: /* Recent publications (2014-2016) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl]; permission required for use.

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*transcription profiling of Bacilli
*''Bacillus subtilis''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2016)==
<pubmed> 27190142, 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
A three-year PhD position in Microbiology: "Phenotypic heterogeneity and population dynamics in biofilms" within the framework of the Priority Programme SPP 1617 - Phenotypic heterogeneity and sociomicrobiology of bacterial populations is available at the Institute of Microbiology, Friedrich Schiller University (FSU) Jena, starting in September 2015. More information at [https://sites.google.com/site/terrestrialbiofilms/home/open-positions].
Contact [mailto:akos-tibor.kovacs@uni-jena.de me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2016-04-07T06:54:29Z

Atkovacs: /* Recent publications (2014-2015) */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl]; permission required for use.

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*transcription profiling of Bacilli
*''Bacillus subtilis''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2016)==
<pubmed> 27044625, 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
A three-year PhD position in Microbiology: "Phenotypic heterogeneity and population dynamics in biofilms" within the framework of the Priority Programme SPP 1617 - Phenotypic heterogeneity and sociomicrobiology of bacterial populations is available at the Institute of Microbiology, Friedrich Schiller University (FSU) Jena, starting in September 2015. More information at [https://sites.google.com/site/terrestrialbiofilms/home/open-positions].
Contact [mailto:akos-tibor.kovacs@uni-jena.de me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

Protein kinases and phosphatases

2015-11-06T07:50:11Z

Atkovacs: /* Reviews */

These enzymes phosphorylate or dephosphorylate other [[phosphoproteins|proteins]]. By definition, they use ATP (or GTP) as the phosphoryl group donor (as opposed to phosphotransferases of the [[PTS|phosphotranferase system]] and the [[phosphorelay]]).

==Protein kinases==
===Protein arginine kinases===
* [[McsB]]

===Protein serine kinases===
* [[HprK]] (has also phosphorylase activity)
* [[PrkC]]
* [[PrkD]]
* [[RsbT]]
* [[RsbW]]
* [[SpoIIAB]]
* [[YabT]]

===Protein tyrosine kinases (see the [http://bykdb.ibcp.fr/BYKdb/BYKdbHelp Bacterial Protein Tyrosine Kinase Database])===
* [[PtkA]]
* [[EpsB]]: similar to [[PtkA]], but has probably no kinase activity

===Protein kinases of [[two-component systems]]===
* [[ComP]]
* [[DegS]]
* [[DesK]]
* [[LiaS]]
* [[YdfH]]
* [[YfiJ]]
* [[YhcY]]
* [[YvfT]]
* [[YxjM]]
* [[BceS]]
* [[CssS]]
* [[NatK]]
* [[PhoR]]
* [[ResE]]
* [[WalK]]
* [[YbdK]]
* [[YcbM]]
* [[YclK]]
* [[YkoH]]
* [[YrkO]]
* [[YvcQ]]
* [[YvrG]]
* [[YxdK]]
* [[CheA]]
* [[CitS]]
* [[DctS]]
* [[GlnK]]
* [[MalK]]
* [[LytS]]
* [[YesM]]
* [[YwpD]]
* [[KinA]]
* [[KinB]]
* [[KinC]]
* [[KinD]]
* [[KinE]]

==Protein phosphatases==
===Protein arginine phosphatases===
* [[YwlE]]

===Protein serine phosphatases===
* [[PrpC]]
* [[RsbP]]
* [[RsbU]]
* [[RsbX]]
* [[SpoIIE]]

===Protein tyrosine phosphatases===
* [[PtpZ]]
* [[YfkJ]]

===Protein aspartate phosphatases controlling the [[phosphorelay]] ===
* [[Spo0E]]: dephosphorylation of [[Spo0A]]
* [[YisI]]: dephosphorylation of [[Spo0A]]
* [[YnzD]]: dephosphorylation of [[Spo0A]]
* [[RapA]]: dephosphorylation of [[Spo0F]]
* [[RapB]]: dephosphorylation of [[Spo0F]]
* [[RapE]]: dephosphorylation of [[Spo0F]]
* [[RapH]]: dephosphorylation of [[Spo0F]]

=Related Lists=
* [[phosphoproteins]]
* [[protein modification]]
* [[two-component systems]]

=Reviews=
<pubmed> 26458398 16209347 21372323 23731382 25625314</pubmed>

Akos T Kovacs

2015-11-06T07:48:19Z

Atkovacs:

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl]; permission required for use.

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*transcription profiling of Bacilli
*''Bacillus subtilis''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications (2014-2015)==
<pubmed> 26458398, 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
A three-year PhD position in Microbiology: "Phenotypic heterogeneity and population dynamics in biofilms" within the framework of the Priority Programme SPP 1617 - Phenotypic heterogeneity and sociomicrobiology of bacterial populations is available at the Institute of Microbiology, Friedrich Schiller University (FSU) Jena, starting in September 2015. More information at [https://sites.google.com/site/terrestrialbiofilms/home/open-positions].
Contact [mailto:akos-tibor.kovacs@uni-jena.de me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

Akos T Kovacs

2015-07-23T11:23:37Z

Atkovacs: /* Recent publications */

[[File:ATKovacs2.jpg‎ ]]

Photo by Wout Overkamp[http://woutoverkamp.nl]; permission required for use.

==Akos T Kovacs==
*Current institution: '''Terrestrial Biofilms''' Research Group, Institute of Microbiology, Friedrich Schiller University Jena
*Faculty member of Jena School for Microbial Communication, '''JSMC'''[http://www.jsmc.uni-jena.de/startpage/]
*Contact: akos-tibor.kovacs@uni-jena.de [mailto:akos-tibor.kovacs@uni-jena.de send mail]

==Research Interests==
*bacterial biofilm development
*phenotypic heterogeneity
*transcription profiling of Bacilli
*''Bacillus subtilis''
*interaction of Bacilli and fungi
*evolution in biofilms
*microbial cooperation and competition

==Publications==
[http://www.ncbi.nlm.nih.gov/pubmed?term=Kovacs%20AT Pubmed]

==Recent publications==
<pubmed> 26152584, 26122431, 25909364, 25886351, 25505463, 25041820, 24033913, 25040940, 24771632, 24694715, 24196425, 24163345, 23924781 </pubmed>

==Homepages==

Terrestrial biofilms group [https://sites.google.com/site/terrestrialbiofilms/]

==Open positions==
A three-year PhD position in Microbiology: "Phenotypic heterogeneity and population dynamics in biofilms" within the framework of the Priority Programme SPP 1617 - Phenotypic heterogeneity and sociomicrobiology of bacterial populations is available at the Institute of Microbiology, Friedrich Schiller University (FSU) Jena, starting in September 2015. More information at [https://sites.google.com/site/terrestrialbiofilms/home/open-positions].
Contact [mailto:akos-tibor.kovacs@uni-jena.de me] for info.

= '''Back to [[Labs working on Bacillus]]''' =

BslA

2015-07-23T11:21:46Z

Atkovacs:

Spo0A

2015-07-23T11:18:14Z

Atkovacs:

KinC

2015-07-23T11:13:43Z

Atkovacs:

* '''Description:''' [[two-component systems|two-component]] sensor kinase, phosphorylates [[Spo0F]] and [[Spo0A]], part of the [[phosphorelay]], governs expression of genes involved in [[biofilm formation]] 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''kinC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ssb ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] sensor kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of [[sporulation]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14490 kinC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=KinC KinC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=kinC kinC]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 6.225
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1284 bp, 428 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[abh]]'', ''[[ykqA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14490 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14490 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14490 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:kinC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=kinC_1518333_1519619_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:kinC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14490]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[protein modification]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[phosphorelay]]}},
{{SubtiWiki category|[[biofilm formation]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[Spo0A regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14490

===Phenotypes of a mutant ===
** defective in [[biofilm formation]] {{PubMed|22882210}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14490&redirect=T BSU14490]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/kinC.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10989]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** autophosphorylation, phosphorylation of [[Spo0F]] as part of the [[phosphorelay]], but also direct phosphorylation of [[Spo0A]] {{PubMed|19114652}}
** mainly active in the younger, outer regions of a colony (with [[KinD]]) {{PubMed|21097618}}
** phosphorylates [[Spo0A]] in response to the presence of surfactin {{PubMed|22882210}}, this has been refuted {{PubMed|25701730}}
** required for initiation of [[sliding]] together with [[KinB]] {{PubMed|26152584}}

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''
** two transmembrane segments
** [[PAS domain]]
** C-terminal histidine phosphotransferase domain

* '''Modification:''' autophosphorylation on a His residue

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** activity is triggered by potassium leakage {{PubMed|19114652}}, this has been refuted {{PubMed|25701730}}
** activity is triggered by polyisoprenoid lipids formed by [[YisP]] {{PubMed|20713508}}

* '''[[SubtInteract|Interactions]]:'''
** [[KinC]]-[[Spo0A]] {{PubMed|19114652}}
** [[KinC]]-[[Spo0F]]

* '''[[Localization]]:'''
** cell membrane (Heterogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
** co-localizes with [[FloT]] in discrete foci in the membrane {{PubMed|20713508}}
** the localization of [[KinC]] in membrane microdomains depends on [[FloA]] and [[FloT]] {{PubMed|22882210}}, this has been refuted {{PubMed|25701730}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14490&redirect=T BSU14490]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P39764 P39764]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14490]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' kinC (according to [http://dbtbs.hgc.jp/COG/prom/kinC.html DBTBS])

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=kinC_1518333_1519619_1 kinC] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigA]] {{PubMed|8002614}}

* '''Regulation:'''
** expressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/8002615 PubMed]

* '''Regulatory mechanism:'''
** [[Spo0A]]: transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/8002615 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A632 ( ''kinC''::''erm''), {{PubMed|3015878}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A632&Search=1A632 BGSC]
** BAL393 (''kinC''::''spc''){{PubMed|26152584}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
== Reviews ==
<pubmed>25934647 25652542</pubmed>

== Original publications ==
<pubmed>26152584,19114652,10094672,11069677,16166384, 20713508,8002615, 16479537 8002614 20946851 20971918 21097618 22882210 23927765 25701730 26152584</pubmed>

[[Category:Protein-coding genes]]

KinB

2015-07-23T11:10:32Z

Atkovacs: /* Basic information/ Evolution */

KinB

2015-07-23T11:10:11Z

Atkovacs:

* '''Description:''' [[two-component systems|two-component]] sensor kinase, phosphorylates [[Spo0F]], part of the [[phosphorelay]], senses changes in respiratory activity 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''kinB''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] sensor kinase
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || initiation of sporulation
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31450 kinB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=KinB KinB]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=kinB kinB]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 47 kDa, 6.682
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1287 bp, 429 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[patB]]'', ''[[kapB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU31450 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU31450 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU31450 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:kinB_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=kinB_3230067_3231353_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:kinB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU31450]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[protein modification]]}},
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[phosphorelay]]}},
{{SubtiWiki category|[[membrane proteins]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[stringent response]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU31450

===Phenotypes of a mutant ===

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU31450&redirect=T BSU31450]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/kinB-kapB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10745]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** autophosphorylation, phosphorylation of [[Spo0F]]
** mainly active in the older, inner regions of a colony (with [[KinA]]) {{PubMed|21097618}}
** sensing potassium level in the medium during initiation of [[sliding]] [[sliding]] {{PubMed|26152584}}

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''
** six transmembrane segments, C-terminal histidine phosphotransferase domain
** selectivity filter sequence of potassium channels that is required for [[sliding]] but not for [[sporulation]] {{PubMed|26152584}}

* '''Modification:''' autophosphorylation on a His residue

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''
** activity is triggered at low respiratory activity, this depends on a functional interaction with the respiration apparatus {{PubMed|23599347}}

* '''[[SubtInteract|Interactions]]:'''
** [[KinB]]-[[Sda]]
** [[KinB]]-[[Spo0F]]
** [[KinB]]-[[CtaC]] {{PubMed|23599347}}
** [[KinB]]-[[QcrC]] {{PubMed|23599347}}

* '''[[Localization]]:''' cell membrane (integral membrane protein) {{PubMed|23599347}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU31450&redirect=T BSU31450]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=3D36 3D36] (from G. stearothermophilus, complex with [[Sda]])

* '''UniProt:''' [http://www.uniprot.org/uniprot/Q08430 Q08430]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU31450]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=
* '''Operon:''' ''[[kinB]]-[[kapB]]'' {{PubMed|8497199}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=kinB_3230067_3231353_1 kinB] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|8497199}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
** induced upon addition of decoyinine (positive [[stringent response]]) {{PubMed|23378509}}

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** JH19980 (''kinB''::''tet'') {{PubMed|9334321}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed>26152584,8576055,16166384,9299348,8497199,10094672,9426145,11069677,12618455,11902725,12618455,7592498, 21097618 19101565 23378509 23599347 26152584</pubmed>

[[Category:Protein-coding genes]]

Sliding

2015-07-23T11:01:31Z

Atkovacs:

Sliding motility is a passive form of surface spreading that does not require an active motor but instead relies on surfactants to reduce surface tension, enabling the colony to spread away from the origin, driven by the outward pressure of cell growth. {{PubMed|20694026}}. Sliding can be observed in wild isolates of ''Bacillus subtilis'' not expressing or deleted for [[hag]] gene {{PubMed|16545127}}. Sliding requires surfactin production and the presence of potassium in the medium {{PubMed|12949115}}. Further, sliding requires various components that are related to biofilm formation {{PubMed|26152584}}.

{{CategoryTree
|Parents=
* 4. [[Lifestyles]]
** 4.1. [[Exponential and early post-exponential lifestyles]]
|Neighbours=
* 4.1.1. [[Motility and chemotaxis]]
* 4.1.2. [[Swarming]]
* 4.1.3. [[Sliding]]
* 4.1.4. [[Biofilm formation]]
* 4.1.5. [[Genetic competence]]
|Related=

|}}

__TOC__
 

==Labs working on sliding==
* [[Daniel Kearns]]
* [[Roberto Kolter]]
* Ray Fall
* [[Akos T Kovacs]]
* [[Roberto Grau]]

==Key genes and operons involved in sliding==
* required for sliding in ''B. subtilis'' NCIB 3610 on MSggN medium
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
** ''[[tasA]]''
** ''[[srfAA]]''
** ''[[srfAB]]''
** ''[[ktrA]]''
** ''[[ktrB]]''
** ''[[ktrC]]''
** ''[[ktrD]]''

* required for sliding in ''B. subtilis'' natto wild type and ''B. subtilis'' NCIB 3610 ''hag'' derivative on LB medium
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
** ''[[bslA]]''
** ''[[srfAA]]''
** ''[[srfAC]]''

* regulation
** [[KinB]]
** [[KinC]]
** [[Spo0A]]

==Important original publications==
<pubmed> 26152584, 25894589, 21784632,19659723,16545127,16321950,12949115</pubmed>

==Key reviews==
<pubmed>20694026, 22092493</pubmed>

=Back to [[categories]]=

Sliding

2015-07-23T11:00:55Z

Atkovacs:

Sliding motility is a passive form of surface spreading that does not require an active motor but instead relies on surfactants to reduce surface tension, enabling the colony to spread away from the origin, driven by the outward pressure of cell growth. {{PubMed|20694026}}. Sliding can be observed in wild isolates of ''Bacillus subtilis'' not expressing or deleted for [[hag]] gene {{PubMed|16545127}}. Sliding requires surfactin production and the presence of potassium in the medium {{PubMed|12949115}}. Further, sliding requires various components that are related to biofilm formation {{PubMed|26152584}}.

{{CategoryTree
|Parents=
* 4. [[Lifestyles]]
** 4.1. [[Exponential and early post-exponential lifestyles]]
|Neighbours=
* 4.1.1. [[Motility and chemotaxis]]
* 4.1.2. [[Swarming]]
* 4.1.3. [[Sliding]]
* 4.1.4. [[Biofilm formation]]
* 4.1.5. [[Genetic competence]]
|Related=

|}}

__TOC__
 

==Labs working on sliding==
* [[Daniel Kearns]]
* [[Roberto Kolter]]
* Ray Fall
* [[Akos T Kovacs]]
* [[Roberto Grau]]

==Key genes and operons involved in sliding==
* required for sliding in ''B. subtilis'' NCIB 3610 on MSggN medium
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
** ''[[tasA]]''
** ''[[srfAA]]''
** ''[[srfAB]]''
** ''[[ktrA]]''
** ''[[ktrB]]''
** ''[[ktrC]]''
** ''[[ktrD]]''

* required for sliding in ''B. subtilis'' natto wild type and ''B. subtilis'' NCIB 3610 ''hag'' derivative on LB medium
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
** ''[[bslA]]''
** ''[[sfrAA]]''
** ''[[sfrAC]]''

* regulation
** [[KinB]]
** [[KinC]]
** [[Spo0A]]

==Important original publications==
<pubmed> 26152584, 25894589, 21784632,19659723,16545127,16321950,12949115</pubmed>

==Key reviews==
<pubmed>20694026, 22092493</pubmed>

=Back to [[categories]]=

Biofilm formation

2015-07-23T10:57:26Z

Atkovacs: /* Important original publications */

Biofilms are the result of the multicellular lifestyle of ''B. subtilis''. They are characterized by the formation of a matrix polysaccharide (poly-N-acetyl glucosamine as a major polysaccharide {{PubMed|26078454}}) and an amyloid-like protein, [[TasA]]. Correction of ''[[sfp]]'', ''[[epsC]]'','' [[swrAA]]'', and ''[[degQ]]'' as well as introduction of ''rapP'' from a plasmid present in NCIB3610 results in biofilm formation in ''B. subtilis'' 168 {{PubMed|21278284}}.

{{CategoryTree
|Parents=
* 4. [[Lifestyles]]
** 4.1. [[Exponential and early post-exponential lifestyles]]
|Neighbours=
* 4.1.1. [[Motility and chemotaxis]]
* 4.1.2. [[Swarming]]
* 4.1.3. [[Sliding]]
* 4.1.4. [[Biofilm formation]]
* 4.1.5. [[Genetic competence]]
|Related=
[[SinR regulon]]
|}}

__TOC__
 
==[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm formation in ''Subti''Pathways]==

==Labs working on biofilm formation==
* [[Roberto Grau]]
* [[Daniel Kearns]]
* [[Roberto Kolter]]
* [[Akos T Kovacs]]
* [[Oscar Kuipers]]
* [[Beth Lazazzera]]
* [[Richard Losick]]
* [[Nicola Stanley-Wall]]
* [[Jörg Stülke]]

==Key genes and operons involved in biofilm formation==
* matrix polysaccharide synthesis {{PubMed|26078454}}:
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
**'' [[galE]]''
* amyloid protein synthesis, secretion and assembly
** ''[[tapA]]-[[sipW]]-[[tasA]]''
* repellent surface layer
** ''[[bslA]]''
* regulation
** [[SlrR]]
** [[SlrA]]
** [[SinR]]
** [[SinI]]
** [[KinC]]
** [[KinD]]
** [[Spo0A]]
** [[PtkA]]
** [[TkmA]]
** [[PtpZ]]
** [[DegU]]
** [[DegQ]]
** [[YmdB]]
** [[FtsH]]
** [[Veg]]
** [[MstX]]
** [[YugO]]

* other proteins required for biofilm formation
** [[AmpS]]
** [[FloT]]
** [[LuxS]]
** [[RemA]]
** [[RemB]]
** [[Rny]]
** [[Sfp/1]]
** [[Sfp/2]]
** [[SpeA]]
** [[SpeD]]
** [[SwrAA]]
** [[YisP]]
** [[YlbF]]
** [[YmcA]]
** [[YvcA]]
** [[YwcC]]
** [[YxaB]]

* other proteins required for efficient pellicle biofilm formation (mutant is out-competed by wild type)
** [[Hag]]
** [[FlgE]]
** [[FliF]]
** [[MotA]]
** [[SigD]]
** [[CheA]]
** [[CheY]]
** [[CheD]]
** [[CheV]]
** [[HemAT]]

==Important original publications==
<pubmed> 26122431, 26152584, 26078454 25870300 26060272 25825426 23271809, 23300252 21267464 21278284 16091050 22232655 22371091 23341623 23406351 25768534 23012477,22934631 23517761 23569226 23564171 25035996 23637960 23645570 24256735 25422306 25680358 25713360 25894589 26200335</pubmed>

==Key reviews==
<pubmed>16787201,24771632, 9891794,19054118,20890834,21109420,20519345,18381896 22024380 20735481 23353768 23791621 23927648 24384602 24909922 26104716 24988880 24608334 25907113</pubmed>

=Back to [[categories]]=

CheV

2015-07-03T06:18:06Z

Atkovacs: /* Biological materials */

* '''Description:''' modulation of [[CheA]] activity in response to attractants 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cheV''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[CheA]] modulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[CheA]] activity
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14010 cheV]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CheV CheV]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 4.617
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 909 bp, 303 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykzT]]'', ''[[kre]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU14010 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU14010 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU14010 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:cheV_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheV_1473605_1474516_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:cheV_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU14010]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription factors and their control]]}}, {{SubtiWiki category|[[phosphoproteins]]}},
{{SubtiWiki category|[[motility and chemotaxis]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigD regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU14010

===Phenotypes of a mutant ===
* ''[[cheV]] [[cheW]]'' double mutants exhibit complete loss of chemotaxis {{PubMed|21098025}}
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14010&redirect=T BSU14010]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cheV.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10823]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[CheW]] (N-terminal domain of CheV)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:''' N-terminal [[CheW]]-like domain, C-terminal two-component receiver domain {{PubMed|11553614}}

* '''Modification:''' the C-terminal two-component receiver domain is phosphorylated on a Asp residue by [[CheA]] {{PubMed|11553614}}

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[CheA]]-[[CheY]] {{PubMed|11553614}}

* '''[[Localization]]:'''
** forms lateral clusters (phosphorylated form), but in the presence of high asparagine concentration (non-phosphorylated form) there is a reversible re-localization to the poles of the cell {{PubMed|21098025}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU14010&redirect=T BSU14010]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P37599 P37599]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU14010]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[cheV]]'' {{PubMed|8169223}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheV_1473605_1474516_1 cheV] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigD]] {{PubMed|8169223}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** in minimal medium, CheV is present with 7,500 +/- 2,000 molecules per cell {{PubMed|21515776}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 1117 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 1764 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''
** DS70 (''cheV''::''mls'' in NCIB3610) {{PubMed|12864845}}
** TB183 ''amyE''::Phy-''sfgfp'' (''cheV''::''mls'' in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB199 ''amyE''::Phy-''mKATE2'' (''cheV''::''mls'' in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>18774298,</pubmed>
==Original publications==
<pubmed> 12864845,26122431, 8169224,8169223,11553614,14731274,21098025, 21515776</pubmed>

[[Category:Protein-coding genes]]

Gert Bange

2015-07-02T13:49:10Z

Atkovacs: Created page with "= Lab head: Gert Bange= '''Additional information''' * [mailto:gert.bange@synmikro.uni-marburg.de send mail] * location: LOEWE-Zentrum für Synthetische Mikrobiologie, Marbur..."

= Lab head: Gert Bange=
'''Additional information'''
* [mailto:gert.bange@synmikro.uni-marburg.de send mail]
* location: LOEWE-Zentrum für Synthetische Mikrobiologie, Marburg, Germany
* Homepage: [http://www.synmikro.com/de/forschung/zellulaere-organisation/gert-bange.html link]

= Publications =
[http://www.ncbi.nlm.nih.gov/pubmed/?term=Bange+G Pubmed]

= Main research interests =
Understanding of regulatory modules, which control the assembly of macromolecular complexes in bacteria (e.g. flagellum, cell division machinery)

= '''Back to [[Labs working on Bacillus]]''' =

Motility and chemotaxis

2015-07-02T13:46:11Z

Atkovacs:

Motility and chemotaxis facilitate swimming and swarming of ''B. subtilis'' {{PubMed|20694026}}. Motility, chemotaxis and aerotaxis facilitate pellicle [[biofilm formation]] in ''B. subtilis'' {{PubMed|26122431}}. Production of flagella is a costly process in ''B. subtilis'' {{PubMed|26122431}}.

{{CategoryTree
|Parents=
* 4. [[Lifestyles]]
** 4.1. [[Exponential and early post-exponential lifestyles]]
|Neighbours=
* 4.1.1. [[Motility and chemotaxis]]
* 4.1.2. [[Swarming]]
* 4.1.3. [[Sliding]]
* 4.1.4. [[Biofilm formation]]
* 4.1.5. [[Genetic competence]]
|Related=
* {{SubtiWiki regulon|[[SigD regulon]]}}
* {{SubtiWiki regulon|[[SlrR regulon]]}}
* [[fla-che operon]]
|}}

==Labs working on motility and chemotaxis ==
* [[Gert Bange]]
* [[Daniel Kearns]]
* [[Akos T Kovacs]]

== Regulation of flagellation ==
* number of flagellar hooks per micrometer of cell length
** in swimming cells: 4 +/- 1 {{PubMed|25538299}}
** in swarming cells: 9 +/- 2 {{PubMed|25538299}}

== Genes in this functional category ==

=== Signal transduction in motility and chemotaxis ===
====Soluble signalling proteins====
* ''[[cheA]]''
* ''[[cheB]]''
* ''[[cheC]]''
* ''[[cheD]]''
* ''[[cheR]]''
* ''[[cheY]]''

====Coupling proteins====
* ''[[cheV]]''
* ''[[cheW]]''

====Soluble chemoreceptors====
* ''[[hemAT]]''
* ''[[yfmS]]''

====Membrane-bound chemoreceptors====
* ''[[mcpA]]''
* ''[[mcpB]]''
* ''[[mcpC]]''
* ''[[tlpA]]''
* ''[[tlpB]]''
* ''[[tlpC]]''
* ''[[yoaH]]''
* ''[[yvaQ]]''

====Additional chemotaxis signal transduction and regulatory proteins====
* ''[[csrA]]''
* ''[[dgrA]]''
* ''[[epr]]''
* ''[[epsE]]''
* ''[[flgM]]''
* ''[[fliY]]''
* ''[[lonA]]''
* ''[[luxS]]''
* ''[[pdeH]]''
* ''[[sigD]]''
* ''[[smiA]]''
* ''[[swrAA/1]]''
* ''[[swrAA/2]]''
* ''[[swrB]]''

=== Flagellar proteins ===
* ''[[flgB]]''
* ''[[flgC]]''
* ''[[flgD]]''
* ''[[flgE]]''
* ''[[flgK]]''
* ''[[flgL]]''
* ''[[flgN]]''
* ''[[flhA]]''
* ''[[flhB]]''
* ''[[flhF]]''
* ''[[flhG]]''
* ''[[flhO]]''
* ''[[flhP]]''
* ''[[fliD]]''
* ''[[fliE]]''
* ''[[fliF]]''
* ''[[fliG]]''
* ''[[fliH]]''
* ''[[fliI]]''
* ''[[fliJ]]''
* ''[[fliK]]''
* ''[[fliL]]''
* ''[[fliM]]''
* ''[[fliP]]''
* ''[[fliQ]]''
* ''[[fliR]]''
* ''[[fliS]]''
* ''[[fliT]]''
* ''[[fliW]]''
* ''[[fliY]]''
* ''[[fliZ]]''
* ''[[hag]]''
* ''[[motA]]''
* ''[[motB]]''
* ''[[motP]]''
* ''[[motS]]''

=== Flagellar proteins/ based on similarity ===
* ''[[ylqH]]''
* ''[[yvyC]]''
* ''[[yvyF]]''

* ''[[yvzB]]''

=== Motility and chemotaxis/ other ===
* ''[[lytC]]''
* ''[[ycdA]]''

==Key original publications==
<pubmed> 24256735 25035996 25538299</pubmed>

==Key reviews==
<pubmed> 26122431, 15187186 18774298 8604438 22092493 25251856 </pubmed>

=Back to [[categories]]=

Motility and chemotaxis

2015-07-02T13:45:20Z

Atkovacs:

Motility and chemotaxis facilitate signal-directed swimming and swarming of ''B. subtilis'' {{PubMed|20694026}}. Motility, chemotaxis and aerotaxis facilitate pellicle [[biofilm formation]] in ''B. subtilis'' {{PubMed|26122431}}. Production of flagella is a costly process in ''B. subtilis'' {{PubMed|26122431}}.

{{CategoryTree
|Parents=
* 4. [[Lifestyles]]
** 4.1. [[Exponential and early post-exponential lifestyles]]
|Neighbours=
* 4.1.1. [[Motility and chemotaxis]]
* 4.1.2. [[Swarming]]
* 4.1.3. [[Sliding]]
* 4.1.4. [[Biofilm formation]]
* 4.1.5. [[Genetic competence]]
|Related=
* {{SubtiWiki regulon|[[SigD regulon]]}}
* {{SubtiWiki regulon|[[SlrR regulon]]}}
* [[fla-che operon]]
|}}

==Labs working on motility and chemotaxis ==
* [[Gert Bange]]
* [[Daniel Kearns]]
* [[Akos T Kovacs]]

== Regulation of flagellation ==
* number of flagellar hooks per micrometer of cell length
** in swimming cells: 4 +/- 1 {{PubMed|25538299}}
** in swarming cells: 9 +/- 2 {{PubMed|25538299}}

== Genes in this functional category ==

=== Signal transduction in motility and chemotaxis ===
====Soluble signalling proteins====
* ''[[cheA]]''
* ''[[cheB]]''
* ''[[cheC]]''
* ''[[cheD]]''
* ''[[cheR]]''
* ''[[cheY]]''

====Coupling proteins====
* ''[[cheV]]''
* ''[[cheW]]''

====Soluble chemoreceptors====
* ''[[hemAT]]''
* ''[[yfmS]]''

====Membrane-bound chemoreceptors====
* ''[[mcpA]]''
* ''[[mcpB]]''
* ''[[mcpC]]''
* ''[[tlpA]]''
* ''[[tlpB]]''
* ''[[tlpC]]''
* ''[[yoaH]]''
* ''[[yvaQ]]''

====Additional chemotaxis signal transduction and regulatory proteins====
* ''[[csrA]]''
* ''[[dgrA]]''
* ''[[epr]]''
* ''[[epsE]]''
* ''[[flgM]]''
* ''[[fliY]]''
* ''[[lonA]]''
* ''[[luxS]]''
* ''[[pdeH]]''
* ''[[sigD]]''
* ''[[smiA]]''
* ''[[swrAA/1]]''
* ''[[swrAA/2]]''
* ''[[swrB]]''

=== Flagellar proteins ===
* ''[[flgB]]''
* ''[[flgC]]''
* ''[[flgD]]''
* ''[[flgE]]''
* ''[[flgK]]''
* ''[[flgL]]''
* ''[[flgN]]''
* ''[[flhA]]''
* ''[[flhB]]''
* ''[[flhF]]''
* ''[[flhG]]''
* ''[[flhO]]''
* ''[[flhP]]''
* ''[[fliD]]''
* ''[[fliE]]''
* ''[[fliF]]''
* ''[[fliG]]''
* ''[[fliH]]''
* ''[[fliI]]''
* ''[[fliJ]]''
* ''[[fliK]]''
* ''[[fliL]]''
* ''[[fliM]]''
* ''[[fliP]]''
* ''[[fliQ]]''
* ''[[fliR]]''
* ''[[fliS]]''
* ''[[fliT]]''
* ''[[fliW]]''
* ''[[fliY]]''
* ''[[fliZ]]''
* ''[[hag]]''
* ''[[motA]]''
* ''[[motB]]''
* ''[[motP]]''
* ''[[motS]]''

=== Flagellar proteins/ based on similarity ===
* ''[[ylqH]]''
* ''[[yvyC]]''
* ''[[yvyF]]''

* ''[[yvzB]]''

=== Motility and chemotaxis/ other ===
* ''[[lytC]]''
* ''[[ycdA]]''

==Key original publications==
<pubmed> 24256735 25035996 25538299</pubmed>

==Key reviews==
<pubmed> 26122431, 15187186 18774298 8604438 22092493 25251856 </pubmed>

=Back to [[categories]]=

Biofilm formation

2015-07-02T13:36:20Z

Atkovacs:

Biofilms are the result of the multicellular lifestyle of ''B. subtilis''. They are characterized by the formation of a matrix polysaccharide (poly-N-acetyl glucosamine as a major polysaccharide {{PubMed|26078454}}) and an amyloid-like protein, [[TasA]]. Correction of ''[[sfp]]'', ''[[epsC]]'','' [[swrAA]]'', and ''[[degQ]]'' as well as introduction of ''rapP'' from a plasmid present in NCIB3610 results in biofilm formation in ''B. subtilis'' 168 {{PubMed|21278284}}.

{{CategoryTree
|Parents=
* 4. [[Lifestyles]]
** 4.1. [[Exponential and early post-exponential lifestyles]]
|Neighbours=
* 4.1.1. [[Motility and chemotaxis]]
* 4.1.2. [[Swarming]]
* 4.1.3. [[Sliding]]
* 4.1.4. [[Biofilm formation]]
* 4.1.5. [[Genetic competence]]
|Related=
[[SinR regulon]]
|}}

__TOC__
 
==[http://subtiwiki.uni-goettingen.de/pathways/biofilm.html Biofilm formation in ''Subti''Pathways]==

==Labs working on biofilm formation==
* [[Roberto Grau]]
* [[Daniel Kearns]]
* [[Roberto Kolter]]
* [[Akos T Kovacs]]
* [[Oscar Kuipers]]
* [[Beth Lazazzera]]
* [[Richard Losick]]
* [[Nicola Stanley-Wall]]
* [[Jörg Stülke]]

==Key genes and operons involved in biofilm formation==
* matrix polysaccharide synthesis {{PubMed|26078454}}:
** ''[[epsA]]-[[epsB]]-[[epsC]]-[[epsD]]-[[epsE]]-[[epsF]]-[[epsG]]-[[epsH]]-[[epsI]]-[[epsJ]]-[[epsK]]-[[epsL]]-[[epsM]]-[[epsN]]-[[epsO]]''
**'' [[galE]]''
* amyloid protein synthesis, secretion and assembly
** ''[[tapA]]-[[sipW]]-[[tasA]]''
* repellent surface layer
** ''[[bslA]]''
* regulation
** [[SlrR]]
** [[SlrA]]
** [[SinR]]
** [[SinI]]
** [[KinC]]
** [[KinD]]
** [[Spo0A]]
** [[PtkA]]
** [[TkmA]]
** [[PtpZ]]
** [[DegU]]
** [[DegQ]]
** [[YmdB]]
** [[FtsH]]
** [[Veg]]
** [[MstX]]
** [[YugO]]

* other proteins required for biofilm formation
** [[AmpS]]
** [[FloT]]
** [[LuxS]]
** [[RemA]]
** [[RemB]]
** [[Rny]]
** [[Sfp/1]]
** [[Sfp/2]]
** [[SpeA]]
** [[SpeD]]
** [[SwrAA]]
** [[YisP]]
** [[YlbF]]
** [[YmcA]]
** [[YvcA]]
** [[YwcC]]
** [[YxaB]]

* other proteins required for efficient pellicle biofilm formation (mutant is out-competed by wild type)
** [[Hag]]
** [[FlgE]]
** [[FliF]]
** [[MotA]]
** [[SigD]]
** [[CheA]]
** [[CheY]]
** [[CheD]]
** [[CheV]]
** [[HemAT]]

==Important original publications==
<pubmed> 26122431, 26078454 25870300 26060272 25825426 23271809, 23300252 21267464 21278284 16091050 22232655 22371091 23341623 23406351 25768534 23012477,22934631 23517761 23569226 23564171 25035996 23637960 23645570 24256735 25422306 25680358 25713360 25894589</pubmed>

==Key reviews==
<pubmed>16787201,24771632, 9891794,19054118,20890834,21109420,20519345,18381896 22024380 20735481 23353768 23791621 23927648 24384602 24909922 26104716 24988880 24608334 25907113</pubmed>

=Back to [[categories]]=

HemAT

2015-07-02T13:27:53Z

Atkovacs:

* '''Description:''' soluble chemotaxis receptor, heme-containing O(2) sensor protein 
{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hemAT''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhfV ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || haem-based aerotactic transducer
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || movement towards oxygen
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU10380 hemAT]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=HemAT HemAT]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.441
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1296 bp, 432 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfU]]'', ''[[yhfW]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU10380 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU10380 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU10380 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:hemAT_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hemAT_1112620_1113918_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hemAT_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU10380]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigD regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU10380

===Phenotypes of a mutant ===
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}
* NCIB3610 ''hemAT'' mutant has higher fitness than ''[[hag]]'' mutant during pellicle formation {{PubMed|26122431}}
* NCIB3610 ''hemAT''-''[[hag]]'' double mutant has similar fitness to single ''[[hag]]'' mutant during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU10380&redirect=T BSU10380]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/hemAT.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13066]

=== Additional information===

=The protein=
* HemAT protein has a moderate oxygen affinity {{PubMed|11821422}}

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** required for full expression of the ''[[phoD]]-[[tatAD]]-[[tatCD]]'' operon {{PubMed|23180473}}

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):''' heme

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[HemAT]]-[[TatAC]] {{PubMed|23180473}}

* '''[[Localization]]:'''
** forms clusters at the cell poles {{PubMed|21515776}}
** homogeneous cytoplsmic distribution in chain-forming cells during the logarithmic phase {{PubMed|23180473}}
** polar foci in individual cells at later growth stages {{PubMed|23180473}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU10380&redirect=T BSU10380]

* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1OR4 1OR4] (in cyano-liganded form), [http://www.rcsb.org/pdb/explore.do?structureId=1OR6 1OR6] {{PubMed|12962628}}

* '''UniProt:''' [http://www.uniprot.org/uniprot/O07621 O07621]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU10380]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''hemAT'' {{PubMed|15033535}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hemAT_1112620_1113918_-1 hemAT] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|15033535}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** in minimal medium, HemAT is present with 19,000 +/- 3,900 molecules per cell {{PubMed|21515776}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 1095 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 1803 {{PubMed|24696501}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 3169 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 966 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 1236 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:'''
** TB239 (''hemAT''::''neo'' in 168) {{PubMed|26122431}}
** TB241 (''hemAT''::''neo'' in NCIB3610) {{PubMed|26122431}}
** TB244 ''amyE''::Phy-''sfgfp'' (''hemAT''::''neo'' in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB243 ''amyE''::Phy-''mKATE2'' (''hemAT''::''neo'' in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=
* [[Akos T Kovacs]]

=Your additional remarks=

=References=
== Reviews ==
<pubmed> 23928310 </pubmed>
== Original publications ==
<pubmed>26122431, 10676961,16819829,11481493,15033535 21515776 23180473 22564695</pubmed>

[[Category:Protein-coding genes]]

SigD

2015-07-02T13:16:38Z

Atkovacs:

* '''Description:''' [[RNA polymerase]] [[sigma factor]] SigD 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''sigD''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''flaB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[RNA polymerase]] [[sigma factor]] SigD
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of flagella, motility, chemotaxis and autolysis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16470 sigD]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=SigD SigD]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.167
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 762 bp, 254 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cheD]]'', ''[[swrB]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16470 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16470 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16470 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:sigD_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigD_1716493_1717257_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:sigD_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16470]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription]]}},
{{SubtiWiki category|[[sigma factors and their control]]}},
{{SubtiWiki category|[[motility and chemotaxis]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[DegU regulon]]}},
{{SubtiWiki regulon|[[SigD regulon]]}},
{{SubtiWiki regulon|[[Spo0A regulon]]}}

=The [[SigD regulon]]=
=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16470

===Phenotypes of a mutant ===
* Inactivation of ''[[alsR]]'', ''[[sigD]]'' and ''[[sigW]]'' increases competitive fitness of ''Bacillus subtilis'' under non-sporulating conditions {{PubMed|22344650}}
* mucoid phenotype due to the overproduction of poly-gamma-glutamate (because of the loss of ''[[motA]]-[[motB]]'' expression) {{PubMed|24296669}}
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16470&redirect=T BSU16470]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10751]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' sigma-70 factor family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:''' interaction with [[FlgM]] inhibits SigD activity {{PubMed|10207036}}

* '''[[SubtInteract|Interactions]]:'''
** [[SigD]]-[[FlgM]] {{PubMed|10207036}}, [[SigD]]-([[RpoB]]-[[RpoC]])

* '''[[Localization]]:'''

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16470&redirect=T BSU16470]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P10726 P10726]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16470]

* '''E.C. number:'''
=== Additional information===

=Expression and regulation=
* '''Operon:''' part of the [[fla-che operon]]
** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}
** ''[[sigD]]-[[swrB]]'' {{PubMed|9335309}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=sigD_1716493_1717257_1 sigD] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''
** ''[[flgB]]'': [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}}
** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}
** ''[[sigD]]'': [[SigA]] {{PubMed|9335309}}

* '''Regulation:''' see [[fla-che operon]]

* '''Regulatory mechanism:''' see [[fla-che operon]]

* '''Additional information:'''

=Biological materials =

* '''Mutant:'''
** 1A716 ( ''sigD''::''cat''), {{PubMed|2832368}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A716&Search=1A716 BGSC]
** DS6420 (marker-less in NCIB3610) {{PubMed|22329926}}
** TB188 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB204 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab

* '''FLAG-tag construct:''' GP948 (ermC, based on [[pGP1087]]), available in the [[Stülke]] lab

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed> 20233302 25251856 </pubmed>

==The [[SigD regulon]]==
<pubmed>15033535,2111808,</pubmed>

==Original publications==
<pubmed> 26122431,22344650 22329926,21097624,22956758 21856853 8955328,7708689,9648743, 8169223,9096206,15175317, 2498284,16357223, 3127378, 9144176,18820022,7602586,2832368,8195064,11987133,,14651647, 9335309 9657996,8157612,15175317 10809682 8932324 20233303 17850253 10207036 16428420 24296669 25099370 24386445</pubmed>

[[Category:Protein-coding genes]]

MotA

2015-07-02T13:14:41Z

Atkovacs:

* '''Description:''' H+-coupled [[MotA]]-[[MotB]] flagellar stator 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''motA''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''mot ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || motility protein (flagellar motor rotation)
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[motility and chemotaxis]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13690 motA]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=MotA MotA]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.01
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 810 bp, 270 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[motB]]'', ''[[clpE]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13690 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13690 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13690 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:motA_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=motA_1434433_1435245_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:motA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13690]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigD regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU13690

===Phenotypes of a mutant ===
* loss of swimming and swarming motility {{PubMed|24296669}}
* mucoid phenotype due to the [[DegU]]-P activated overexpression of the ''[[capB]]-[[capC]]-[[capA]]-[[capE]]'' operon and resulting overproduction of poly-gamma-glutamate {{PubMed|24296669}}
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13690&redirect=T BSU13690]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/motAB.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10688]

=== Additional information===
* A mutation was found in this gene after evolution under relaxed selection for sporulation {{PubMed|21821766}}

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' motA family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[MotP]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''

* '''[[Cofactors]]:'''

* '''Effectors of protein activity:'''
** the interaction with [[DgrA]] inhibits [[MotA]] activity {{PubMed|22821967}}

* '''[[SubtInteract|Interactions]]:'''
** [[MotA]]-[[MotB]]
** [[DgrA]]-[[MotA]] {{PubMed|22821967}}

* '''[[Localization]]:''' cell membrane (according to Swiss-Prot)

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13690&redirect=T BSU13690]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P28611 P28611]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13690]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[motA]]-[[motB]]'' {{PubMed|6313226}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=motA_1434433_1435245_-1 motA] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|6313226}}
* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 100 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 613 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''
** 1A631 ( ''motA''::''erm''), {{PubMed|3015878}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A631&Search=1A631 BGSC]
** 1A923 ( ''motA''::''erm''), {{PubMed|12813063}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A923&Search=1A923 BGSC]
** DS7498 (marker-less in NCIB3610) {{PubMed|24296669}}
** TB193 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB210 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 26122431, 6313226 21821766 22821967 24296669 24771657 </pubmed>
[[Category:Protein-coding genes]]

FliF

2015-07-02T13:12:41Z

Atkovacs:

* '''Description:''' flagellar basal-body M-ring protein, membrane anchor of the basal body 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''fliF''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellar basal-body M-ring protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || movement and chemotaxis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16210 fliF]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=FliF FliF]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 59 kDa, 4.37
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1608 bp, 536 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fliE]]'', ''[[fliG]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16210 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16210 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16210 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:fliF_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fliF_1692496_1694106_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:fliF_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16210]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[DegU regulon]]}},
{{SubtiWiki regulon|[[SigD regulon]]}},
{{SubtiWiki regulon|[[Spo0A regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16210

===Phenotypes of a mutant ===
* mucoid phenotype due to the overproduction of poly-gamma-glutamate {{PubMed|24296669}}
* no secretion of [[FlgM]], permanent inhibition of [[SigD]] {{PubMed|25313396}}
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16210&redirect=T BSU16210]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10240]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** required for correct localization of [[FliM]] {{PubMed|23190039}}

* '''Protein family:''' fliF family (according to Swiss-Prot)

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''

* '''[[Cofactors]]:'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[FliF]]-[[FliG]] {{PubMed|25313396}}

* '''[[Localization]]:'''
** cell membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16210&redirect=T BSU16210]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P23447 P23447]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16210]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' part of the [[fla-che operon]] (see there for regulation)
** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=fliF_1692496_1694106_1 fliF] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}}

* '''Regulation:''' see [[fla-che operon]]

* '''Regulatory mechanism:''' see [[fla-che operon]]

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 68 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 595 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''
** DS7080 (marker-less in NCIB3610) {{PubMed|24296669}}
** TB192 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB208 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=

<pubmed> 26122431, 1905667,17850253,14651647,18763711, 9657996,8157612,15175317 23190039 24296669 25313396 24386445 25843804</pubmed>

[[Category:Protein-coding genes]]

FlgE

2015-07-02T13:10:40Z

Atkovacs:

* '''Description:''' flagellar hook protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''flgE''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''flgG ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellar hook protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || movement and chemotaxis
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16290 flgE]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 27 kDa, 4.734
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[flgD]]'', ''[[ylzI]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16290 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16290 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16290 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:flgE_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=flgE_1700182_1700976_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:flgE_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16290]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[DegU regulon]]}},
{{SubtiWiki regulon|[[SigD regulon]]}},
{{SubtiWiki regulon|[[Spo0A regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16290

===Phenotypes of a mutant ===
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16290&redirect=T BSU16290]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10249]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
* lack of [[SigD]]-dependent gene expression (no ''[[hag]]'' expression), no motility {{PubMed|22730131}}

* '''Protein family:''' flagella basal body rod proteins family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[FlhO]], [[FlhP]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''

* '''[[Localization]]:''' bacterial flagellum basal body (according to Swiss-Prot), extracellular (no signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed], membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16290&redirect=T BSU16290]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P23446 P23446]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16290]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=
* '''Operon:''' part of the [[fla-che operon]] (see there for regulation)
** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=flgE_1700182_1700976_1 flgE] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''
** ''[[flgB]]'': [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}}
** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}

* '''Regulation:''' see [[fla-che operon]]

* '''Regulatory mechanism:''' see [[fla-che operon]]

* '''Additional information:'''
** number of protein molecules per cell (minimal medium with glucose and ammonium): 1780 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 3035 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''
** DS4681 (marker-less in NCIB3610) {{PubMed|22730131}}
** TB187 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB203 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
<pubmed> 26122431, 14651647,18957862 18763711, 9657996,8157612,15175317 17850253 24386445 22730131</pubmed>

[[Category:Protein-coding genes]]

Hag

2015-07-02T13:08:20Z

Atkovacs:

* '''Description:''' flagellin protein, about 20,000 subunits make up one flagellum 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''hag''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || flagellin protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || [[motility and chemotaxis]]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35360 hag]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=Hag Hag]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: [http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=Hag Hag]'''
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 32 kDa, 4.782
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 912 bp, 304 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvyC]]'', ''[[csrA]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU35360 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU35360 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU35360 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:hag_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hag_3634987_3635901_-1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:hag_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU35360]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}},
[[most abundant proteins]]

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[CsrA regulon]]}},
{{SubtiWiki regulon|[[ScoC regulon]]}},
{{SubtiWiki regulon|[[SigD regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU35360

===Phenotypes of a mutant ===

* no swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}
* few hours delay in pellicle development {{PubMed|26122431}}
* mutant has increased fitness in planktonic culture when competed with the wild-type NCIB3610 strain {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35360&redirect=T BSU35360]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/hag.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10655]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:''' bacterial flagellin family (according to Swiss-Prot)

* '''Paralogous protein(s):''' [[YvzB]] (C-terminal domain of Hag)

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''

* '''[[Cofactors]]:'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[FlhA]]-[[Hag]] {{PubMed|20534509}}
** [[FlhA]]-([[FliS]]-[[Hag]]) {{PubMed|20534509}}
** [[FliS]]-[[Hag]] {{PubMed|20534509}}
** [[FliW]]-[[Hag]] {{PubMed|21895793}}

* '''[[Localization]]:'''
** extracellular (no signal peptide), major component of the secretome [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
** membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU35360&redirect=T BSU35360]

* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=3A5X 3A5X] (from ''Salmonella typhimurium'', 42% identity)

* '''UniProt:''' [http://www.uniprot.org/uniprot/P02968 P02968]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU35360]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[hag]]'' {{PubMed|2498284}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=hag_3634987_3635901_-1 hag] {{PubMed|22383849}}

* '''[[Sigma factor]]:''' [[SigD]] {{PubMed|2498284}}

* '''Regulation:'''
** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]

* '''Regulatory mechanism:'''
** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12730172 PubMed]
** [[CsrA]]: translation inhibition {{PubMed|17555441}}
** [[ScoC]]: transcription repression {{PubMed|19118355}}

* '''Additional information:'''
** the ''[[hag]]'' gene is strongly overexpressed in a ''[[ymdB]]'' mutant (loss of bistable gene expression) {{PubMed|21856853}}
** belongs to the 100 [[most abundant proteins]] {{PubMed|15378759}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 150241 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 280953 {{PubMed|24696501}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 9552 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 11147 {{PubMed|21395229}}
** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 24114 {{PubMed|21395229}}

=Biological materials =
* '''Mutant:''' GP901 (aphA3), GP902 (tet) {{PubMed|21856853}}, both available in [[Jörg Stülke]]'s lab
** 1A915 ( ''hag''::''cat''), {{PubMed|19202088}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A915&Search=1A915 BGSC]
** 1A783 ( ''hag''::''erm''), {{PubMed|2174860}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A783&Search=1A783 BGSC]
** 1A842 ( ''hag''::''kan''), {{PubMed|14762011}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A842&Search=1A842 BGSC]
** DS1677 (marker-less in NCIB3610) {{PubMed|18566286}}
** TB191 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB207 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''
** expression in ''B. subtilis'', in [[pBQ200]]: pGP1089, available in [[Jörg Stülke]]'s lab

* '''lacZ fusion:''' pGP1035 (in [[pAC6]]), pGP755 (in [[pAC7]]), there is also a series of promoter deletion variants in [[pAC6]] and [[pAC7]] {{PubMed|21856853}}, all available in [[Jörg Stülke]]'s lab

* '''GFP fusion:''' BP494 (bglS:: (hag-promoter-cfp-aphA3)), BP496 (amyE:: (hag-promoter-iyfp-cat)), available in [[Jörg Stülke]]'s lab

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=
* [[Daniel Kearns]]

=Your additional remarks=

=References=
==Reviews==
<pubmed>22672726 25251856 </pubmed>
==Original Publications==
<pubmed> 18566286,26122431,23144244 21602220 21856853 2498284,9648743,9096206,7708689,19202088, 18763711, 21895793 10809682 19118355 17555441 20534509 15378759</pubmed>
[[Category:Protein-coding genes]]

McpC

2015-07-02T13:03:55Z

Atkovacs:

* '''Description:''' membrane-bound chemotaxis receptor for proline, methyl-accepting chemotaxis protein 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''mcpC''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''prg71 ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || methyl-accepting chemotaxis protein
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || control of chemotaxis threonine, glycine, serine, lysine, valine and arginine
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13950 mcpC]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=McpC McpC]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 71 kDa, 5.174
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1962 bp, 654 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykwB]]'', ''[[ykwC]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU13950 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU13950 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU13950 DNA_with_flanks]
|-
|-
|-
|colspan="2" | '''Genetic context''' [[Image:mcpC_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcpC_1463628_1465595_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:mcpC_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU13950]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[motility and chemotaxis]]}},
{{SubtiWiki category|[[membrane proteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[SigD regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU13950

===Phenotypes of a mutant ===
* not essential for pellicle biofilm formation and mutant has similar fitness to the wild-type strain when competed during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13950&redirect=T BSU13950]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/mcpC.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11533]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''
** deaminated [[McpC]] stimulates phosphorylation of [[CheA]] {{PubMed|22931217}}

* '''Protein family:'''

* '''Paralogous protein(s):'''

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''Domains:'''

* '''Modification:'''
** deamination of Gln-609 (by [[CheD]]) {{PubMed|22931217}}, deaminated [[McpC]] stimulates phosphorylation of [[CheA]] {{PubMed|22931217}}

* '''Cofactor(s):'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[CheD]]-[[McpC]], deamination of Gln-609 in [[McpC]] {{PubMed|22931217}}
** [[McpC]]-[[ArtP]], for chemotaxis to lysine and arginine {{PubMed|23038252}}
** [[McpC]]-[[MetQ]], for chemotaxis to methionine {{PubMed|23038252}}
** [[McpC]]-[[YckB]], for chemotaxis to tryptophan {{PubMed|23038252}}

* '''[[Localization]]:'''
** cell membrane {{PubMed|18763711,21515776}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU13950&redirect=T BSU13950]

* '''Structure:'''

* '''UniProt:''' [http://www.uniprot.org/uniprot/P54576 P54576]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU13950]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=

* '''Operon:''' ''[[mcpC]]'' {{PubMed|9353924}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=mcpC_1463628_1465595_1 mcpC] {{PubMed|22383849}}

* '''Sigma factor:''' [[SigD]] {{PubMed|9353924}}

* '''Regulation:'''

* '''Regulatory mechanism:'''

* '''Additional information:'''
** in minimal medium, McpC is present with 2,800 +/- 640 molecules per cell {{PubMed|21515776}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 236 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 990 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''
** DS180 (''mcpC''::''mls'' in NCIB3610) {{PubMed|12864845}}
** TB184 ''amyE''::Phy-''sfgfp'' (''mcpC''::''mls'' in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB200 ''amyE''::Phy-''mKATE2'' (''mcpC''::''mls'' in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
'''Additional publications:''' {{PubMed|22931217}}
<pubmed>12864845,26122431,15317802,8251536,9353924,15544802,6137212,9721285,2505839,2105313,12603740,23038252,18763711 9721285, 21515776</pubmed>

[[Category:Protein-coding genes]]

CheY

2015-07-02T13:01:12Z

Atkovacs:

* '''Description:''' [[two-component systems|two-component]] response regulator, modulation of flagellar switch bias 

{| align="right" border="1" cellpadding="2"
|-
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''cheY''
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cheB ''
|-
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || [[two-component systems|two-component]] response regulator
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || modulation of flagellar switch bias
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16330 cheY]
|-
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CheY CheY]
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 13 kDa, 4.746
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 360 bp, 120 aa
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[fliY]]'', ''[[fliZ]]''
|-
|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16330 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16330 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16330 DNA_with_flanks]
|-
|colspan="2" | '''Genetic context''' [[Image:cheY_context.gif]]
<div align="right"> This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</div>
|-
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheY_1703834_1704196_1 Expression at a glance]'''   {{PubMed|22383849}} [[Image:cheY_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16330]]
|-
|}

__TOC__
 
 
 
 

= [[Categories]] containing this gene/protein =
{{SubtiWiki category|[[transcription factors and their control]]}},
{{SubtiWiki category|[[motility and chemotaxis]]}},
{{SubtiWiki category|[[phosphoproteins]]}}

= This gene is a member of the following [[regulons]] =
{{SubtiWiki regulon|[[CodY regulon]]}},
{{SubtiWiki regulon|[[DegU regulon]]}},
{{SubtiWiki regulon|[[SigD regulon]]}},
{{SubtiWiki regulon|[[Spo0A regulon]]}}

=The gene=

=== Basic information ===

* '''Locus tag:''' BSU16330

===Phenotypes of a mutant ===
* not essential for pellicle biofilm formation, but mutant is outcompeted by the wild-type strain when competed during pellicle formation {{PubMed|26122431}}

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16330&redirect=T BSU16330]

* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/fla-che.html]

* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10258]

=== Additional information===

=The protein=

=== Basic information/ Evolution ===

* '''Catalyzed reaction/ biological activity:'''

* '''Protein family:'''

* '''Paralogous protein(s):''' [[YneI]]

=== Extended information on the protein ===

* '''Kinetic information:'''

* '''[[Domains]]:'''

* '''Modification:'''
** phosphorylated by [[CheA]] on an Asp residue
** dephosphorylated by [[CheC]] {{PubMed|23226535}}

* '''[[Cofactors]]:'''

* '''Effectors of protein activity:'''

* '''[[SubtInteract|Interactions]]:'''
** [[CheY]]-P-[[CheC]] {{PubMed|23226535}}
** [[CheA]]-[[CheY]]

* '''[[Localization]]:'''
** cytoplasm (according to Swiss-Prot)

=== Database entries ===
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16330&redirect=T BSU16330]

* '''Structure:''' [http://pdb.org/pdb/explore/explore.do?structureId=1tmy 1TMY] ([[CheY]] from ''Thermotoga maritima'')

* '''UniProt:''' [http://www.uniprot.org/uniprot/P24072 P24072]

* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16330]

* '''E.C. number:'''

=== Additional information===

=Expression and regulation=
* '''Operon:''' part of the [[fla-che operon]]
** ''[[flgB]]-[[flgC]]-[[fliE]]-[[fliF]]-[[fliG]]-[[fliH]]-[[fliI]]-[[fliJ]]-[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|9657996,8157612,15175317}}
** ''[[ylxF]]-[[fliK]]-[[flgD]]-[[flgE]]-[[fliL]]-[[fliM]]-[[fliY]]-[[cheY]]-[[fliZ]]-[[fliP]]-[[fliQ]]-[[fliR]]-[[flhB]]-[[flhA]]-[[flhF]]-[[flhG]]-[[cheB]]-[[cheA]]-[[cheW]]-[[cheC]]-[[cheD]]-[[sigD]]-[[swrB]]'' {{PubMed|20233303}}

* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cheY_1703834_1704196_1 cheY] {{PubMed|22383849}}

* '''[[Sigma factor]]:'''
** ''[[flgB]]'': [[SigA]] {{PubMed|9657996}}, [[SigD]] {{PubMed|9657996}}
** ''[[ylxF]]'': [[SigD]] {{PubMed|20233303}}

* '''Regulation:''' see [[fla-che operon]]

* '''Regulatory mechanism:''' see [[fla-che operon]]

* '''Additional information:'''
** in minimal medium, CheY is present with 7,100 +/- 1,000 molecules per cell {{PubMed|21515776}}
** number of protein molecules per cell (minimal medium with glucose and ammonium): 1164 {{PubMed|24696501}}
** number of protein molecules per cell (complex medium with amino acids, without glucose): 2117 {{PubMed|24696501}}

=Biological materials =

* '''Mutant:'''
** 1A798 ( ''cheY''::''cat''), {{PubMed|1905718}}, available at [http://pasture.asc.ohio-state.edu/BGSC/getdetail.cfm?bgscid=1A798&Search=1A798 BGSC]
** DS6870 (marker-less in NCIB3610) {{PubMed|25313396}}
** TB191 ''amyE''::Phy-''sfgfp'' (marker-less in NCIB3610 with constitutive expressed ''sfgfp'') {{PubMed|26122431}}
** TB207 ''amyE''::Phy-''mKATE2'' (marker-less in NCIB3610 with constitutive expressed ''mKATE2'') {{PubMed|26122431}}

* '''Expression vector:'''

* '''lacZ fusion:'''

* '''GFP fusion:'''

* '''two-hybrid system:'''

* '''Antibody:'''

=Labs working on this gene/protein=

=Your additional remarks=

=References=
==Reviews==
<pubmed>25313396, 26122431, 19494578,,10094672 20122866 16224120 </pubmed>

==Original Publications==
<pubmed>,17908686,10196193,17850253,12920116,8369293,9194713,14651647, 9657996,8157612,15175317, 14749334,20080618,17675386 21515776 24386445</pubmed>

[[Category:Protein-coding genes]]